I strongly doubt it. Shockwave plays an important role in the aligned countinuity such as the space bridge and Insecticons in Fall of Cybertron not to mention being one of Megatron's inner circle. That and he's one of the most iconic TF characers out there so they can't just toss him aside like that. To do so would be not only bad writing but a major mistake.

And if it's indeed a flashback episode what's to say he won't re-appear to the present? Just because it's a flashback doesn't mean he'll be dead. Likely in stasis for now.

They reused Cliffjumper's model for Tailgate, had him alive for a few minutes, had him as a zombie for a while, and had him for at least two flashbacks (counting the Shockwave one). They aren't just gonna put Shockwave in a random flashback and never use the design again. If they wanted to do that they'd probably just do the typical hand drawn flashback. Especially if the flashback or Shockwave's appearance is a small portion of the episode, or if he transforms.